I'm not seeing any problems with the MXF files I have, so it's probably a good idea to make the very smallest project you can that still exhibits this problem and send it to Adobe (via the bug report - provide a link where they can grab it). That way they have the best chance of seeing what's happening.
I have seen this once in CS6, but for me it helped clearing out the cache.
That was on Canon XF, mxf files.
Because I experience the "tearing issue", http://forums.adobe.com/thread/1009064?start=0&tstart=0 , on my mxf files, I transcode to avi wrapper with UT codec, so I have not had it mre than once.
Have you tried to use tha cam util to offload the card / spanned clips and ten import them into the proect, instead of importing via the mediabrowser or prelude (if you have production premium)
I have experienced this exact same problem with files from my NanoFlash recorder.
I went back to CS5.5.